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References · full bibliography33 sources · grouped by mechanism

Every claim, and where it comes from

This is the complete source list behind the Rebel Reef work, grouped by the mechanism each paper supports. Every entry is verified against its DOI. The Science page cites these inline; the Data & Researchers page has the methods and datasets. Where a source is grey literature or a field-survey record rather than a peer-reviewed paper, it is marked.

The site itself, Banco Capiro / Tela Bay

  1. Cramp R, Exton DA, Bodmer MDV, Lubbock N, Reverter M (2025). Steep decline in Diadema antillarum populations in Honduras' Mesoamerican barrier reef (2014-2022) and its impact on benthic communities. Coral Reefs 44(6):2135-2145. doi:10.1007/s00338-025-02778-8 — the key longitudinal study of Banco Capiro; the urchin-loss-then-coral-decline record.
  2. Bodmer MDV, Rogers AD, Speight MR, Lubbock N, Exton DA (2015). Using an isolated population boom to explore barriers to recovery in the keystone Caribbean coral reef herbivore Diadema antillarum. Coral Reefs 34(4):1011-1021. doi:10.1007/s00338-015-1329-4 — origin of the "one of the healthiest reefs in the Caribbean" baseline.
  3. Bodmer MDV, Wheeler PM, Anand P, Cameron SE, Hintikka S, Cai W, Borcsok AO, Exton DA (2021). The ecological importance of habitat complexity to the Caribbean coral reef herbivore Diadema antillarum: three lines of evidence. Scientific Reports 11:9382. doi:10.1038/s41598-021-87232-9
  4. Operation Wallacea (2024). Honduras Marine Research Report 2024. 42 pp. — grey literature; the field-survey time series for Tela Bay coral cover and Diadema density (Op Wallacea / Coral Reef Alliance, 2011-2024).

The 2022 Diadema die-off, herbivory and grazing collapse

  1. Mumby PJ, Hastings A, Edwards HJ (2007). Thresholds and the resilience of Caribbean coral reefs. Nature 450:98-101. doi:10.1038/nature06252 — the coral / macroalgae / turf bistability model we use.
  2. Hewson I, Ritchie IT, Evans JS, Altera A, Behringer D, Brandt M, Croquer A, et al. (2023). A scuticociliate causes mass mortality of Diadema antillarum in the Caribbean Sea. Science Advances 9:eadg3200. doi:10.1126/sciadv.adg3200 — the causative agent of the 2022 die-off.
  3. Hylkema A, Kitson-Walters K, Kramer PR, Patterson JT, Roth L, Sevier MLB, Vega-Rodriguez M, Warham MM, et al. (2023). The 2022 Diadema antillarum die-off event: comparisons with the 1983-1984 mass mortality. Frontiers in Marine Science 9:1067449. doi:10.3389/fmars.2022.1067449
  4. Lessios HA (1988). Mass mortality of Diadema antillarum in the Caribbean: what have we learned? Annual Review of Ecology and Systematics 19:371-393. doi:10.1146/annurev.es.19.110188.002103

Turbid and marginal-reef refugia, the turbidity-shading mechanism

  1. Browne NK, Bauman AG (2023). Marginal reef systems: resilience in a rapidly changing world. Diversity 15(6):703. doi:10.3390/d15060703
  2. Cacciapaglia C, van Woesik R (2016). Climate-change refugia: shading reef corals by turbidity. Global Change Biology 22:1145-1154. doi:10.1111/gcb.13166
  3. Sully S, van Woesik R (2020). Turbid reefs moderate coral bleaching under climate-related temperature stress. Global Change Biology 26(3):1367-1373. doi:10.1111/gcb.14948
  4. Lucas CC, Teixeira CEP, Braga MDA, Carlos Júnior F, Paiva SV, Gurgel AL, Rossi S, Soares MO (2023). Heatwaves and a decrease in turbidity drive coral bleaching in Atlantic marginal equatorial reefs. Frontiers in Marine Science 10:1061488. doi:10.3389/fmars.2023.1061488 — the counter-case: when turbidity drops during a heatwave, 91% of colonies bleached. Our episodic-shading finding predicts this vulnerability.
  5. Smith EG, et al. (2020). Low Symbiodiniaceae diversity in a turbid marginal reef environment. Coral Reefs 39:545-553. doi:10.1007/s00338-020-01956-0 — the skeptical note: turbidity is not an unambiguous benefit.

Heterotrophy and bleaching resilience, the feeding mechanism

  1. Grottoli AG, Rodrigues LJ, Palardy JE (2006). Heterotrophic plasticity and resilience in bleached corals. Nature 440:1186-1189. doi:10.1038/nature04565
  2. Grottoli AG, Warner ME, Levas SJ, Aschaffenburg MD, Schoepf V, McGinley M, Baumann J, Matsui Y (2014). The cumulative impact of annual coral bleaching can turn some coral species winners into losers. Global Change Biology 20:3823-3833. doi:10.1111/gcb.12658 — the caveat: repeat bleaching erodes the heterotrophic buffer.

Heat-tolerant symbionts, the Durusdinium mechanism

  1. Baker AC (2003). Flexibility and specificity in coral-algal symbiosis. Annual Review of Ecology, Evolution, and Systematics 34:661-689. doi:10.1146/annurev.ecolsys.34.011802.132417
  2. Berkelmans R, van Oppen MJH (2006). The role of zooxanthellae in the thermal tolerance of corals: a "nugget of hope" for coral reefs in an era of climate change. Proceedings of the Royal Society B 273:2305-2312. doi:10.1098/rspb.2006.3567
  3. Silverstein RN, Cunning R, Baker AC (2017). Tenacious D: Symbiodinium in clade D remain in reef corals at both high and low temperature extremes despite impairment. Journal of Experimental Biology 220(7):1192-1196. doi:10.1242/jeb.148239
  4. Palacio-Castro AM, Smith TB, Brandtneris V, Snyder GA, van Hooidonk R, Maté JL, Manzello D, Glynn PW, Fong P, Baker AC (2023). Increased dominance of heat-tolerant symbionts creates resilient coral reefs in near-term ocean warming. PNAS 120:e2202388120. doi:10.1073/pnas.2202388120
  5. Hussain A, Hari Krishna Kumar S, Ashwin Kumar A, Prathiviraj R, Renjith K, Seghal Kiran G, Selvin J (2025). Delineating the emergence of thermally tolerant Symbiodiniaceae genotypes across the dominant coral species of a turbid reef. Science of the Total Environment 963:178255. doi:10.1016/j.scitotenv.2024.178255 — turbid-reef symbionts, the closest analog to our hypothesis.
  6. Rajesh Kannan M, Balakrishnan R, Thillaichidambaram M, Natesan S, Paramasamy G, Prakash S, Chockalingam Muthiah R (2022). Probing the thermo-tolerant endosymbiont genus Durusdinium (clade D) in the scleractinian corals of Palk Bay. Biologia 78:255-264. doi:10.1007/s11756-022-01235-z

Runoff, thermal stress, and the data and models

  1. Fabricius KE (2005). Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Marine Pollution Bulletin 50:125-146. doi:10.1016/j.marpolbul.2004.11.028
  2. Hughes TP, et al. (2017). Global warming and recurrent mass bleaching of corals. Nature 543:373-377. doi:10.1038/nature21707
  3. Liu G, et al. (2014). Reef-scale thermal stress monitoring of coral ecosystems: NOAA Coral Reef Watch. Remote Sensing 6:11579-11606. doi:10.3390/rs61111579 — source of the 5 km SST and Degree Heating Weeks (via PacIOOS ERDDAP).
  4. Safaie A, et al. (2018). High frequency temperature variability reduces the risk of coral bleaching. Nature Communications 9:1671. doi:10.1038/s41467-018-04074-2
  5. Lellouche J-M, et al. (2021). The Copernicus global 1/12° oceanic and sea-ice GLORYS12 reanalysis. Frontiers in Earth Science 9:698876. doi:10.3389/feart.2021.698876
  6. Delandmeter P, van Sebille E (2019). The Parcels v2.0 Lagrangian framework for community ocean modelling. Geoscientific Model Development 12:3571-3584. doi:10.5194/gmd-12-3571-2019

Acute hypoxia and white-water reef mortality (the June-2023 precedents)

  1. Kealoha AK, Doyle SM, Shamberger KEF, Sylvan JB, Hetland RD, DiMarco SF (2020). Localized hypoxia may have caused coral reef mortality at the Flower Garden Banks. Coral Reefs 39:119-132. doi:10.1007/s00338-019-01883-9 — the closest analog to Tela's June-2023 event.
  2. Johnston MA, Nuttall MF, Eckert RJ, et al. (2019). Localized coral reef mortality event at East Flower Garden Bank, Gulf of Mexico. Bulletin of Marine Science 95(2):239-250. doi:10.5343/bms.2018.0057
  3. Doyle SM, Self MJ, Hayes J, et al. (2022). Microbial community dynamics provide evidence for hypoxia during a coral reef mortality event. Applied and Environmental Microbiology 88(9):e0034722. doi:10.1128/aem.00347-22
  4. Altieri AH, Harrison SB, Seemann J, Collin R, Diaz RJ, Knowlton N (2017). Tropical dead zones and mass mortalities on coral reefs. PNAS 114(14):3660-3665. doi:10.1073/pnas.1621517114 — reef hypoxia events are underreported ~10x; Bocas del Toro 2017 killed ~90% coral.
  5. Ohde T, Dadou I (2018). Seasonal and annual variability of coastal sulphur plumes in the northern Benguela upwelling system. PLOS ONE 13(2):e0192140. doi:10.1371/journal.pone.0192140 — upwelling H₂S "sulphur eruptions" make satellite-visible milky-white plumes with mass mortality.
  6. Ohde T (2018). Coastal sulfur plumes off Peru during El Niño, La Niña, and neutral phases. Geophysical Research Letters 45:7075-7083. doi:10.1029/2018GL077618

This is a pre-expedition modeling draft (v1), not yet peer-reviewed. Two look-alike papers were checked and excluded as not Tela Bay. The Science page shows which mechanism each source supports; the adversarial review that stress-tested these claims is in the repository.